An array of double-layer silica nanoparticles with two different length scales was introduced onto the glass substrates for investigating the effect of surface morphology on wettability. Silica nanoparticles of 7, 12, 20, and 40 nm in diameters were individually functionalized using 3-aminopropyltriethoxysilane or 3-glycidoxypropyltrimethoxysilane. Silica nanoparticles functionalized with the complementary amine and epoxy groups were deposited alternately on glass surfaces to obtain durable and covalently bound dual-size double-layer silica nanoparticle coatings. Order of the deposition of nanoparticles for the fabrication of dual-size double-layer coatings was found to be the most determinant factor on surface roughness and hence the wettability. Deposition of the bigger nanoparticles on top of smaller ones resulted in rougher surfaces and consequently higher hydrophobicity. Based upon these findings, it is now possible to fine-tune surface roughness and subsequent wettability by controlling the size ratio of dual-size double-layer silica nanoparticles.